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Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-PHOSPHATE(PYRANOSE form) and magnesium ion
Analyse Crystal structure of transketolase in complex with thiamine diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M7I
- Type
- protein
- Length
- 632 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- Q0P7Y3
- Ligands
- TPP, RP5, MG
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transketolase (EC 2.2.1.1) | protein | 632 | 47% helix, 14% strand | Q0P7Y3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · chains A
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.57 | 0.85 | 26 | TPP, MG |
| 2 | 255 | 0.56 | 0.77 | 54 | empty |
| 3 | 174 | 0.49 | 0.76 | 19 | empty |
| 4 | 82 | 0.45 | 0.81 | 16 | empty |
| 5 | 71 | 0.34 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3M7I · Crystal structure of transketolase in complex with thiamine diphosphate… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q0P7Y3
- Elsewhere: RCSB PDB 3M7I · PDBe 3M7I · UniProt Q0P7Y3
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